JAL-2446 merged to spike branch

[jalview.git] / src / jalview / analysis / Dna.java

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index d1901c3..2106dc2 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -45,7 +45,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
-import java.util.Map;
 
 public class Dna
 {
@@ -685,7 +684,7 @@ public class Dna
          */
         MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
 
-        transferCodedFeatures(selection, newseq, map, null, null);
+        transferCodedFeatures(selection, newseq, map);
 
         /*
          * Construct a dataset sequence for our new peptide.
@@ -754,25 +753,15 @@ public class Dna
 
   /**
    * Given a peptide newly translated from a dna sequence, copy over and set any
-   * features on the peptide from the DNA. If featureTypes is null, all features
-   * on the dna sequence are searched (rather than just the displayed ones), and
-   * similarly for featureGroups.
+   * features on the peptide from the DNA.
    * 
    * @param dna
    * @param pep
    * @param map
-   * @param featureTypes
-   *          hash whose keys are the displayed feature type strings
-   * @param featureGroups
-   *          hash where keys are feature groups and values are Boolean objects
-   *          indicating if they are displayed.
    */
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
-          MapList map, Map<String, Object> featureTypes,
-          Map<String, Boolean> featureGroups)
+          MapList map)
   {
-    SequenceFeature[] sfs = dna.getSequenceFeatures();
-    Boolean fgstate;
     DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
             DBRefSource.DNACODINGDBS);
     if (dnarefs != null)
@@ -786,24 +775,15 @@ public class Dna
         }
       }
     }
-    if (sfs != null)
+    for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
     {
-      for (SequenceFeature sf : sfs)
-      {
-        fgstate = (featureGroups == null) ? null : featureGroups
-                .get(sf.featureGroup);
-        if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
-                && (fgstate == null || fgstate.booleanValue()))
+        if (FeatureProperties.isCodingFeature(null, sf.getType()))
         {
-          if (FeatureProperties.isCodingFeature(null, sf.getType()))
+          // if (map.intersectsFrom(sf[f].begin, sf[f].end))
           {
-            // if (map.intersectsFrom(sf[f].begin, sf[f].end))
-            {
 
-            }
           }
         }
-      }
     }
   }
 
@@ -852,13 +832,18 @@ public class Dna
     char[] originalSequence = sequence.toCharArray();
     int length = originalSequence.length;
     char[] reversedSequence = new char[length];
-
+    int bases = 0;
     for (int i = 0; i < length; i++)
     {
-      reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
+      char c = complement ? getComplement(originalSequence[i])
               : originalSequence[i];
+      reversedSequence[length - i - 1] = c;
+      if (!Comparison.isGap(c))
+      {
+        bases++;
+      }
     }
-    SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
+    SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
     return reversed;
   }
 
@@ -873,7 +858,12 @@ public class Dna
   public static char getComplement(char c)
   {
     char result = c;
-    switch (c) {
+    switch (c)
+    {
+    case '-':
+    case '.':
+    case ' ':
+      break;
     case 'a':
       result = 't';
       break;